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2018-12-06 - I2K 2018 Dresden Hackathon

    From Monday, December 3, 2018 through Friday, December 7, 2018, the Max Planck Institute of Molecular Cell Biology and Genetics hosts ~10 developers at the Center for Systems Biology in Dresden, Germany for a hackathon to develop KNIME Image Processing and ImageJ2/Fiji core infrastructure and plugins.

    Gitter channel: https://gitter.im/juglab/Hack1812

    Topics / Technical Discussions

    TensorFlow (Debo, Curtis, Benny)

    • Plan for TensorFlow: ship native libs both CPU and GPU in lib/ directly;
    • TensorFlow update sites and reconcile to new TF version – add tests

    SCIFIO (Gabriel, Curtis)

    • Create samples.scif.io, migrate LOCI samples, update scif.io website with a table of samples
    • Update scifio-bf-compat to split the mega-format into one per reader/writer


    • Code of conduct - https://help.github.com/articles/adding-a-code-of-conduct-to-your-project/> - <http://openrespect.org/ (It’s written by the author of The Art of Community)
    • Update fiji.sc, imagej.net/Fiji, etc. with revised maintainership info

    Google Scholar: citation count badges on wiki pages

    • What to do about NanoJ using google analytics – i.e. should we have usage stats?
      • [Action item] Ask Ricardo Henriques about it
      • Consider what to write onto code of conduct about what should be allowed

    Meet at later point in time—and who is going to do it

    • What to do about the two different logos: ImageJ vs. Fiji
    • Upstream Java issues – send something shortly after January 15
      • [Action item for Ulrik] Writeup from Ulrik and Stephan S. about JavaFX
      • [Action item for Ulrik] Writeup from Tobias about Unsafe


    • doi in maven pom
    • citation badge on wiki pages

    Servers (Gaby, Debo, Curtis)

    • Server infrastructure overview with Gaby

    rsync mirror to pacific.mpi-cbg.de

    Labkit as Labeling Editor for KNIME Image Processing

    • Node for editing labels in KNIME based on Labkit was created.
    • Work is not entirely finish. We plan to finish this work during the Ostrava Hackathon.
    • Labkit was extended, and is now able to handle multiple images.
    • A labeling datatype to store labels, and track modifications was developed.

    Simple ImageJ API

    • Discussion between: Deborah, Robert, Curtis, Matthias
    • How can we make the scripting in ImageJ2 easier?
    • Setup a table, of scripting examples in IJ1 and IJ2. Improve the IJ2 API where ever it’s obviously required.
    • Write a SimpleIJ gateway, that provides really simple methods for the most frequent tasks in ImageJ.
    • A ImageJ2 script recorder could improve the IJ2 API, as it clearly shows where the API is to verbos.

    Big Data Server

    • Discussion Tobias, Gabriella and Matthias about a mechanism for secure user authentication in Big Data Server (and ImageJ Server).
    • It’s needed by biologists, that want to share there data with specific users.
    • ImageJ Server would also benefit, if the access to the API could be authenticated in a similar way.

    Octtree Like, Compressed, Fast, Bitmaps for Imglib2

    • Tobias develops a data structure to store bitmap. For iteration, efficient pixels access and little memory foot print at the same time.
    • Such data structures can be used to better express labels in imglib2. Even instance segmentations that consist of millions of labels, can be accessed efficiently if a cell image like cache is used.

    HTTPS (Debo, Curtis, Gaby, Tobi)

    • HTTPS java-version-check
    • move list of update sites to a GitHub repository – off the wiki

    Updater/Launcher (Debo, Curtis)

    • Add version to db.xml.gz schema
    • Make the updater smart enough to support serving maven artifacts
    • Migrate “make fiji package” to imagej updater
    • improve “make package” to only zip up non-update-site things (“online mode”)
    • Eliminate native launcher in favor of javafx + java-launches-java scheme

    Plot Service (Matthias, Curtis)

    • Get it merged to scijava-common / scijava-ui-swing
    • https://forum.image.sc/t/error-noclassdeffounderror-net-imagej-table-table/21369/7


    • Merge script editor PRs

    add “browse javadoc” and “browse source” options for selected code? e.g. on IOService opens DefaultIOService on GitHub or javadoc.scijava.org

    • Finish algorithms branch of imagej-mesh – Move imagej-ops mesh package and algorithms into imagej-mesh – See WIP commit message on algorithms branch – Update imagej-ops to call migrated routines


    • Remove modern mode from GUI (Debo, Curtis)
    • Labkit + KNIME (Matthias, Tim-Oliver, others)
    • KNIME+TensorFlow+Server (Tim-Oliver, Benny)
    • Ilastik tracking (Carsten, Mangal)
    • Scenery + KNIME including BigVolumeViewer (Ulrik, Gabriel)
    • Image metadata (Carsten, Marcel)